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(-) Description

Title :  CRYSTAL STRUCTURE OF OCTAPRENYL PYROPHOSPHATE SYNTHASE FROM HYPERTHERMOPHILIC THERMOTOGA MARITIMA
 
Authors :  R. T. Guo, C. J. Kuo, C. C. Chou, T. P. Ko, H. L. Shr, P. H. Liang, A. H. - J. Wang
Date :  13 Nov 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Trans-Type Prenyltransferase, Thermophilic (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. T. Guo, C. J. Kuo, C. C. Chou, T. P. Ko, H. L. Shr, P. H. Liang, A. H. -J. Wang
Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima And Mechanism Of Product Chain Length Determination
J. Biol. Chem. V. 279 4903 2004
PubMed-ID: 14617622  |  Reference-DOI: 10.1074/JBC.M310161200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OCTOPRENYL-DIPHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 2.5.1.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET32XA-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: OCTAPRENYL PYROPHOSPHATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (4x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 2 (1, 28)
No.NameCountTypeFull Name
1SO428Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:60 , GLU A:61 , ASP A:62 , HOH A:1181BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWAREARG A:150 , GLY B:101 , ASP B:102BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREHIS A:74 , ARG A:91 , HOH A:1052 , HOH A:1090 , HOH A:1117 , HOH A:1136BINDING SITE FOR RESIDUE SO4 A 1003
4AC4SOFTWAREGLY B:60 , GLU B:61 , ASP B:62 , HOH B:1083 , HOH B:1212BINDING SITE FOR RESIDUE SO4 B 1004
5AC5SOFTWAREGLY A:101 , ASP A:102 , ARG B:150BINDING SITE FOR RESIDUE SO4 B 1005
6AC6SOFTWARETRP A:251 , HOH A:1044 , ARG B:88BINDING SITE FOR RESIDUE SO4 B 1006
7AC7SOFTWARELYS B:41 , HIS B:74 , HOH B:1045 , HOH B:1046 , HOH B:1049BINDING SITE FOR RESIDUE SO4 B 1007

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V4E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V4E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V4E)

(-) Exons   (0, 0)

(no "Exon" information available for 1V4E)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:280
 aligned with Q9X1M1_THEMA | Q9X1M1 from UniProtKB/TrEMBL  Length:299

    Alignment length:280
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
         Q9X1M1_THEMA     9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRDF 288
               SCOP domains d1v4ea_ A: Octoprenyl-diphosphate synthase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1v4eA00 A:9-288 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4e A   9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRDF 288
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288


Chain B from PDB  Type:PROTEIN  Length:280
 aligned with Q9X1M1_THEMA | Q9X1M1 from UniProtKB/TrEMBL  Length:299

    Alignment length:280
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
         Q9X1M1_THEMA     9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRDF 288
               SCOP domains d1v4eb_ B: Octoprenyl-diphosphate synthase                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1v4eB00 B:9-288 Farnesyl Diphosphate Synthase                                                                                                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4e B   9 NSYELEKVKERIEQILSQFFPEQIMKDLPLYGKMLRVRLSILSFKNRGVEIGEDAISSLAALELVHLASLLHDDVIDGARFRRGKETINFMYGDKAAVAAGDLVLVSAFHTVEEIGNNKLRRAFLNVIGKMSEAELIEQLSRYKPITKEEYLRIVEGKSGALFGLALQLPALLEGELGEDLYNLGVTIGTIYQMFDDIMDFAGMEKIGKDGFLDLKNGVASFPLVTAMEKFPEARQMFENRDWSGLMSFMREKGILKECEETLKVLVKNVIIENSWLRDF 288
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288
   Legend:   → Mismatch (orange background)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V4E)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9X1M1_THEMA | Q9X1M1)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.

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  1v4e
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  2.5.1.11
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9X1M1_THEMA | Q9X1M1: 1v4h 1v4i 1v4j 1v4k 1vg2 1vg3 1vg4 1vg6 1vg7 1wkz 1wl0 1wl1 1wl2 1wl3 2azl

(-) Related Entries Specified in the PDB File

1v4h THE SAME PROTEIN(F52A)
1v4i THE SAME PROTEIN(F132A)
1v4j THE SAME PROTEIN(V73Y)
1v4k THE SAME PROTEIN(S77F)